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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaacctcagtacttgatagagatcttagattgaaaatgctccctgaaatctagtccctgacagatgttctgaatctggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAGGCAGGGCCTACGCAGCTGAGTTTGTATTAGGATGTCTTTTACTCCCATG

Basic information

species Oryza sativa
transcript LOC_Os01g14140.2
intron # 3
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|10931503|gb|AU161777.1|AU161777
EST:     AACTGCCTACTTCCAGAACTCAGGCTNCTCGTCCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGA-
genomic: AACTG-CTACTTCCAGAACTCA-GCT-CTCGT-CGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|163927940|gb|EG713516.1|EG713516
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88322926|gb|CI548020.1|CI548020
EST:     GCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: GCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88539552|gb|CI469514.1|CI469514
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88975387|gb|CI023638.1|CI023638
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|86260931|gb|CI066606.1|CI066606
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88521021|gb|CI448675.1|CI448675
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|66913626|gb|CX100474.1|CX100474
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88239801|gb|CI238963.1|CI238963
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88741066|gb|CI764574.1|CI764574
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGC
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGC
EST: gi|88238941|gb|CI239955.1|CI239955
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88851563|gb|CI671003.1|CI671003
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCT
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCT
EST: gi|5667448|gb|AU077690.1|AU077690
EST:     TGGAACTGCTACTTTCCNGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: TGGAACTGCTAC-TTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
EST: gi|88511157|gb|CI438663.1|CI438663
EST:     CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAA                         GTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG
genomic: CTGGAACTGCTACTTCCAGAACTCAGCTCTCGTCGTGCAGTCTGACCCAAgtatttaacc ... ggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaatgctccctgaaatctagtccctgacagatgttctgaatctggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAGGCAGGGCCTACGCAGCTGAGTTTGTATTAGGATGTCTTTTACTCCCATG
                       ccctgac  putative branch site (score: 3)
              aaatcta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaacctcagtacttgatagagatcttagattgaaaatgctccctgaaatctagtccctgacagatgttctgaatctggttttgcagGTTATGGTTCCTGCACGTACTACTGATTTTAAAACTGAGGTCGAGGTCGAGGCAGGGCCTACGCAGCTGAGTTTGTATTAGGATGTCTTTTACTCCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG